Boyle AP - Search Results

1

Comprehensive enhancer-target gene assignments improve gene set level interpretation of genome-wide regulatory data.

Qin T, Lee C, Li S, Cavalcante RG, Orchard P, Yao H, Zhang H, Wang S, Patil S, Boyle AP, Sartor MA. Qin T, et al. Among authors: boyle ap. Genome Biol. 2022 Apr 26;23(1):105. doi: 10.1186/s13059-022-02668-0. Genome Biol. 2022. PMID: 35473573 Free PMC article.

2

Linking disease associations with regulatory information in the human genome.

Schaub MA, Boyle AP, Kundaje A, Batzoglou S, Snyder M. Schaub MA, et al. Among authors: boyle ap. Genome Res. 2012 Sep;22(9):1748-59. doi: 10.1101/gr.136127.111. Genome Res. 2012. PMID: 22955986 Free PMC article.

3

Annotation of functional variation in personal genomes using RegulomeDB.

Boyle AP, Hong EL, Hariharan M, Cheng Y, Schaub MA, Kasowski M, Karczewski KJ, Park J, Hitz BC, Weng S, Cherry JM, Snyder M. Boyle AP, et al. Genome Res. 2012 Sep;22(9):1790-7. doi: 10.1101/gr.137323.112. Genome Res. 2012. PMID: 22955989 Free PMC article.

4

A proximity-based graph clustering method for the identification and application of transcription factor clusters.

Spadafore M, Najarian K, Boyle AP. Spadafore M, et al. Among authors: boyle ap. BMC Bioinformatics. 2017 Nov 29;18(1):530. doi: 10.1186/s12859-017-1935-y. BMC Bioinformatics. 2017. PMID: 29187152 Free PMC article.

5

Genome-wide Study of Atrial Fibrillation Identifies Seven Risk Loci and Highlights Biological Pathways and Regulatory Elements Involved in Cardiac Development.

Nielsen JB, Fritsche LG, Zhou W, Teslovich TM, Holmen OL, Gustafsson S, Gabrielsen ME, Schmidt EM, Beaumont R, Wolford BN, Lin M, Brummett CM, Preuss MH, Refsgaard L, Bottinger EP, Graham SE, Surakka I, Chu Y, Skogholt AH, Dalen H, Boyle AP, Oral H, Herron TJ, Kitzman J, Jalife J, Svendsen JH, Olesen MS, Njølstad I, Løchen ML, Baras A, Gottesman O, Marcketta A, O'Dushlaine C, Ritchie MD, Wilsgaard T, Loos RJF, Frayling TM, Boehnke M, Ingelsson E, Carey DJ, Dewey FE, Kang HM, Abecasis GR, Hveem K, Willer CJ. Nielsen JB, et al. Among authors: boyle ap. Am J Hum Genet. 2018 Jan 4;102(1):103-115. doi: 10.1016/j.ajhg.2017.12.003. Epub 2017 Dec 28. Am J Hum Genet. 2018. PMID: 29290336 Free PMC article.

6

Cell Specificity of Human Regulatory Annotations and Their Genetic Effects on Gene Expression.

Varshney A, VanRenterghem H, Orchard P, Boyle AP, Stitzel ML, Ucar D, Parker SCJ. Varshney A, et al. Among authors: boyle ap. Genetics. 2019 Feb;211(2):549-562. doi: 10.1534/genetics.118.301525. Epub 2018 Dec 28. Genetics. 2019. PMID: 30593493 Free PMC article.

7

Poly-Enrich: count-based methods for gene set enrichment testing with genomic regions.

Lee CT, Cavalcante RG, Lee C, Qin T, Patil S, Wang S, Tsai ZTY, Boyle AP, Sartor MA. Lee CT, et al. Among authors: boyle ap. NAR Genom Bioinform. 2020 Mar;2(1):lqaa006. doi: 10.1093/nargab/lqaa006. Epub 2020 Feb 6. NAR Genom Bioinform. 2020. PMID: 32051932 Free PMC article.

8

TRACE: transcription factor footprinting using chromatin accessibility data and DNA sequence.

Ouyang N, Boyle AP. Ouyang N, et al. Among authors: boyle ap. Genome Res. 2020 Jul;30(7):1040-1046. doi: 10.1101/gr.258228.119. Epub 2020 Jul 6. Genome Res. 2020. PMID: 32660981 Free PMC article.

9

Cas9 targeted enrichment of mobile elements using nanopore sequencing.

McDonald TL, Zhou W, Castro CP, Mumm C, Switzenberg JA, Mills RE, Boyle AP. McDonald TL, et al. Among authors: boyle ap. Nat Commun. 2021 Jun 11;12(1):3586. doi: 10.1038/s41467-021-23918-y. Nat Commun. 2021. PMID: 34117247 Free PMC article.

10

Prioritization of regulatory variants with tissue-specific function in the non-coding regions of human genome.

Dong S, Boyle AP. Dong S, et al. Among authors: boyle ap. Nucleic Acids Res. 2022 Jan 11;50(1):e6. doi: 10.1093/nar/gkab924. Nucleic Acids Res. 2022. PMID: 34648033 Free PMC article.

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